157 research outputs found
Registration of Standardized Histological Images in Feature Space
In this paper, we propose three novel and important methods for the
registration of histological images for 3D reconstruction. First, possible
intensity variations and nonstandardness in images are corrected by an
intensity standardization process which maps the image scale into a standard
scale where the similar intensities correspond to similar tissues meaning.
Second, 2D histological images are mapped into a feature space where continuous
variables are used as high confidence image features for accurate registration.
Third, we propose an automatic best reference slice selection algorithm that
improves reconstruction quality based on both image entropy and mean square
error of the registration process. We demonstrate that the choice of reference
slice has a significant impact on registration error, standardization, feature
space and entropy information. After 2D histological slices are registered
through an affine transformation with respect to an automatically chosen
reference, the 3D volume is reconstructed by co-registering 2D slices
elastically.Comment: SPIE Medical Imaging 2008 - submissio
Multi-Planar Deep Segmentation Networks for Cardiac Substructures from MRI and CT
Non-invasive detection of cardiovascular disorders from radiology scans
requires quantitative image analysis of the heart and its substructures. There
are well-established measurements that radiologists use for diseases assessment
such as ejection fraction, volume of four chambers, and myocardium mass. These
measurements are derived as outcomes of precise segmentation of the heart and
its substructures. The aim of this paper is to provide such measurements
through an accurate image segmentation algorithm that automatically delineates
seven substructures of the heart from MRI and/or CT scans. Our proposed method
is based on multi-planar deep convolutional neural networks (CNN) with an
adaptive fusion strategy where we automatically utilize complementary
information from different planes of the 3D scans for improved delineations.
For CT and MRI, we have separately designed three CNNs (the same architectural
configuration) for three planes, and have trained the networks from scratch for
voxel-wise labeling for the following cardiac structures: myocardium of left
ventricle (Myo), left atrium (LA), left ventricle (LV), right atrium (RA),
right ventricle (RV), ascending aorta (Ao), and main pulmonary artery (PA). We
have evaluated the proposed method with 4-fold-cross validation on the
multi-modality whole heart segmentation challenge (MM-WHS 2017) dataset. The
precision and dice index of 0.93 and 0.90, and 0.87 and 0.85 were achieved for
CT and MR images, respectively. While a CT volume was segmented about 50
seconds, an MRI scan was segmented around 17 seconds with the GPUs/CUDA
implementation.Comment: The paper is accepted to STACOM 201
Ball-Scale Based Hierarchical Multi-Object Recognition in 3D Medical Images
This paper investigates, using prior shape models and the concept of ball
scale (b-scale), ways of automatically recognizing objects in 3D images without
performing elaborate searches or optimization. That is, the goal is to place
the model in a single shot close to the right pose (position, orientation, and
scale) in a given image so that the model boundaries fall in the close vicinity
of object boundaries in the image. This is achieved via the following set of
key ideas: (a) A semi-automatic way of constructing a multi-object shape model
assembly. (b) A novel strategy of encoding, via b-scale, the pose relationship
between objects in the training images and their intensity patterns captured in
b-scale images. (c) A hierarchical mechanism of positioning the model, in a
one-shot way, in a given image from a knowledge of the learnt pose relationship
and the b-scale image of the given image to be segmented. The evaluation
results on a set of 20 routine clinical abdominal female and male CT data sets
indicate the following: (1) Incorporating a large number of objects improves
the recognition accuracy dramatically. (2) The recognition algorithm can be
thought as a hierarchical framework such that quick replacement of the model
assembly is defined as coarse recognition and delineation itself is known as
finest recognition. (3) Scale yields useful information about the relationship
between the model assembly and any given image such that the recognition
results in a placement of the model close to the actual pose without doing any
elaborate searches or optimization. (4) Effective object recognition can make
delineation most accurate.Comment: This paper was published and presented in SPIE Medical Imaging 201
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